[Chimera-users] surface calculation failed on new laptop

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 3 13:53:52 PDT 2017


Hi Paul,
Sorry about the difficulties.  I can’t speak as to the hardware issues, but the following alternatives to MSMS surface calculations in Chimera should not be susceptible to the numerical falilures:

(1) “molmap” to make an isosurface, but shape will not be quite the same as the solvent-excluded molecular surface
See under #3 in the surface workarounds page: 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>

(2) semi-secret grid method of generating a solvent-excluded molecular surface. See
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010595.html>

In both cases, be VERY careful to only specify the protein atoms, for example:

molmap #0&protein 4 gridSpacing 0.5
- or -
surf #0&protein grid .5

…otherwise all the other atoms (solvent, ligands, etc.) will be assimilated into the blob. Also, these alternative-method surfaces in Chimera aren't automatically associated with atoms, so to get coloring by atom or residue attribute, you have to color the underlying atoms by said attribute, then use the Color Zone tool (or “scolor” command with zone option) to propagate the atom coloring to nearby surface patches.  You can also color them by map values (electrostatic potential, etc.).

ChimeraX uses the same grid method as mentioned above, but it is more fully integrated and easier to specify/color by atom.  However, as you probably know, ChimeraX does not yet have coloring by attribute.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 3, 2017, at 1:22 PM, Paul van Erp <pbgvanerp at gmail.com> wrote:
> 
> Dear chimera users and developers,
> 
> Recently I purchased a new laptop. One of the primary uses of this laptop is rendering structures using chimera and running VR simulations of these structures. I've used the new ChimeraX successfully for this. However I also use the old version of chimera for structure visualization, coloring according to attribute lists and I create morph models between structures. The new laptop is unable to calculate virtually any surface. 
> 
> I've gone through the various troubleshooting pages and tried many things. None seem to be effective. 
> 
> Is it possible that the surface calculation would be more successful on a different computer? Also would this depend on the hardware? or might a similar computer from a different brand suffice? 
> 
> Any help you could offer would be greatly appreciated. 
> Thanks in advance,
> Regards,
> Paul van Erp




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